SeSAMe supports Mammal 40 array natively.
res_grn = sesameDataDownload("GSM4411982_Grn.idat.gz")
res_red = sesameDataDownload("GSM4411982_Red.idat.gz")
sset = readIDATpair(sprintf("%s/GSM4411982", res_red$dest_dir))## Warning in ExperimentHub(localHub = TRUE): DEPRECATION: As of ExperimentHub (>1.17.2), default caching location has changed.
## Problematic cache: /home/kabilan/.cache/ExperimentHub
## See ExperimentHub vignette section on 'Default Caching Location Update'
## Warning in ExperimentHub(localHub = FALSE): DEPRECATION: As of ExperimentHub (>1.17.2), default caching location has changed.
## Problematic cache: /home/kabilan/.cache/ExperimentHub
## See ExperimentHub vignette section on 'Default Caching Location Update'
## Warning in ExperimentHub(localHub = TRUE): DEPRECATION: As of ExperimentHub (>1.17.2), default caching location has changed.
## Problematic cache: /home/kabilan/.cache/ExperimentHub
## See ExperimentHub vignette section on 'Default Caching Location Update'
Preprocess the sigset to produce beta values. The standard noob, dyeBiasCorrTypeINorm works as expected:
Retrieve beta values using the following commands